Introduction

Rice (Oryza sativa L.) as the primary staple food for half of the global population, with increasing the living standard of rice consumers, the demand of premium rice grain quality is increasing along with the climate change, agricultural land limitation, and also growing population up to 9 billion expected by 2050 ^{1, 2, 3, 4, 5, 6, 7, 8}. Therefore, identification of genomics regions related to the rice grain quality traits has become a primary objective in the rice breeding program and receiving big attention from rice consumers and producers. Genome-wide association study (GWAS) by using diverse rice population and large number of molecular markers have successfully detected genomic regions related to the rice grain quality traits. These grain quality traits belong to the complex quantitative traits that are regulated by multiple genes and affected by environmental conditions ^{9, 10, 11}. Recently, rice grain quality traits including appearance quality (grain length, grain width, grain length to width ratio, grain weight, and percent chalkiness), nutritional quality (protein content, lipid content, minerals, vitamins, and phenols), cooking and eating quality (amylose content, gelatinization temperature, and gel consistency), and milling quality (brown rice recovery, milled rice recovery, and head rice recovery) become the major considerations of rice producers for capturing consumers demands of high-quality rice in the rice marketplace ^{12, 13, 14, 15, 16}.

The most crucial rice grain quality trait that effect rice market acceptability is related to the grain appearance ^{17, 18, 19}. Rice grain appearance also influence the rice yield that associated with grain length, grain width, and grain weight ^{20, 21, 22}. Grain length and grain width define grain shape and size ^{23, 24}. Slender rice grain consider having grain length to width ratio of three and above ^{25, 26}. Rice grain quality preferences differs among the countries and cultures ²⁷. Rice consumers in India, Southern China, Pakistan, Bangladesh, Sri Lanka, Southeastern Asian countries, and USA prefer slender and long grains with texture fluffy to harder, and contain intermediate to high amylose content. Meanwhile, rice consumers in Japan, South Korea, and Northern China prefer short and round grain with soft and sticky texture, and also with low amylose content ^{28, 29, 30}.

An undesirable trait of the rice quality is grain chalkiness that reduce palatability, cooking and eating quality of cooked rice ³¹. Grain chalkiness is an opaque area in the back, core, and belly of the rice grain. Chalky rice grains are prone to breakage during milling due to loosely packed, large, and round starch granules ³². Percentage of rice grain with chalkiness also influence market acceptability ^{32, 33}. Rice grain with more than 2% chalkiness is not accepted by rice market ^{34, 35}. The rice price with different grain appearance varies among regions ^{36, 37}. The most rice market prefer rice grains with translucent endosperms ³⁸.

Eating and cooking quality of rice grain associated with cooked rice textures as stickiness and firmness, and also the easiness of cooking. Eating and cooking quality of rice influenced by the grain composition, including starch (80-85%), protein (4-10%), and lipid (1%) that showed high variation among rice varieties ^{28, 39}. Rice starch consist of two components, amylose and amylopectin that associated with texture, gel consistency, pasting viscosity, and gelatinization temperature ^{40, 41}. Amylose content influences the physicochemical characteristics of starch that influence eating and cooking properties ⁴². Cooked rice texture and processing characteristics are influenced by amylose content and gelatinization temperature ³³. Gelatinization temperature showed a strong correlation with the cooking time ⁴³. Rice grain that has high gelatinization temperature needs longer cooking times, more water, and less sticky texture compared to low gelatinization temperature rice ^{44, 45}. According to the rice consumers preferences, the high-quality rice cultivars has low to intermediated gelatinization temperature ^{46, 47}. Based on the amylose content, rice grain can be classified into waxy (0-20%), low waxy (12-20%), intermediate waxy (20-25%), and high waxy (25-33%) ^{48, 19}. One of the rice quality trait that associated with higher rice price is aroma. Jasmine and Basmati rice belong to the aromatic rice that contain phenolic compound 2-acetyl-1-pyrroline (2-AP) which correlated with rice fragrance, such as popcorn-like aroma, milky aromas, sweet nutty, and cracker-like roasted ^{27, 49, 50, 51}.

Rice grain quality traits determine the rice price and rice grain market classes in commercial markets. Advanced molecular breeding methods such as GWAS supported by the development of next-generation sequencing methods and -omics technologies led to identify genomic regions associated with the rice grain quality traits effectively ^{47, 52, 53, 54}. By understanding the genetic architecture of the rice quality traits could increase breeding efficiency to develop rice variety with high-quality based on rice consumers in competitive rice commercial markets that can satisfy rice consumers. In this review, emphasis on the crucial rice quality traits based on the rice consumers preferences, including grain length (GL), grain width (GW), grain length to width ratio (RGLW), grain weight (GWT), amylose content (AC), protein content (PC), and also gelatinization temperature (GT).  

Phenotypic Variation and Correlation of Grain Quality Traits in Rice

A wide range of phenotypic variation, normal distributions, and also transgressive segregants were observed for all evaluated grain quality traits, including GL, GW, RGLW, GWT, AC, PC, GT, and also ECQ suggesting that these traits were quantitatively inherited ^{55, 56}. Transgressive segregant formation is important for rice quality traits improvement due to the availability of novel alleles and genes for improving the quality traits ^{17, 57, 58, 59}. Wide ranges of phenotypic variations were present in the GL of rice from 6 until 12 cm ^{17, 21, 22, 34, 36, 57, 60, 61, 62, 63, 64, 65, 66, 67}; GW with range 2-4 cm ^{17, 21, 22, 34, 36, 57, 60, 61, 62, 64, 65, 68}; range of RGLW from 2-3.5 ^{17, 21, 34, 36, 47, 57, 62, 64, 67}; GWT range 23-27 g ^{21, 61, 62, 64, 65, 66}; AC range 0.8-661% ^{31, 47, 60, 61, 69}; range of PC 0.5-12% ^{61, 69}; and also GT range 60-70^oC ^{47, 60, 61}. Therefore, understanding the genetic architecture of phenotypic variation in rice quality traits by using GWAS method is important for improving the rice quality based on the rice consumers preferences.

Low to high correlations were observed among the rice quality traits. Positive and strong correlations were detected between GL and GWT suggesting that GL has the strongest effect on grain weight than the other rice grain quality traits ^{13, 23, 57}. Meanwhile, GW more contributes on the grain thickness. GL showed low and negatively correlated with GW. Additionally, GL has moderate and positive correlation with RGLW. Positive and very weak correlations were found between GWT and RGLW ^{17, 57, 70}. GL and GW were all showed strong and positive correlation with RGLW and GWT. Low correlation detected between grain appearance traits (GL, GW, RGLW, and GWT) and AC. Correlation between grain appearance (GL, GW, RGLW, and GWT) and GT also low ³⁶. Pairwise correlation analysis among the quality traits showed that all of the correlations are similar across the years ^{36, 71}. Based on these results suggesting that long grain rice would have lower GW, higher GW and RGLW. Therefore, it is possible to develop rice varieties with different rice grain shape according to the consumers preferences in the different rice markets.

Genome-Wide Association Study of Grain Quality Traits in Rice

A powerful tool and an effective approach to identify loci associated with the rice grain quality traits is a GWAS ^{21, 72, 73, 74, 75, 76, 77, 78, 79, 80}. Developing rice varieties with desired characteristics of rice to satisfy rice consumers could be more effective by using GWAS ^{45, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94}. The first GWAS associated with rice grain quality traits were conducted by Huang et al. (2010)⁶⁰ by using 517 rice diverse landraces that genotyped by ~3.6 million SNPs. GWAS detected major and minor quantitative trait loci (QTLs) correlated with the grain quality traits. GWAS also fine mapped of QTLs that lead to identify genes regulated QTLs of grain quality traits and guide to develop rice varieties with high-quality grains to satisfy the rice consumers preferences ^{47, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118}. In this review article, we will explore the recent development of identification of genomic regions associated with the rice grain quality traits from 2010 until 2022. These rice grain quality traits including grain length (GL), grain width (GW), grain length to width ratio (RGLW), grain weight (GWT), amylose content (AC), protein content (PC), and also gelatinization temperature (GT).

Grain rice appearance such as GL, GW, and RGLW belong to the most stable quality traits and have high heritability ¹¹⁹. A lot of GWAS have been done for grain rice appearance traits (GL, GW, and RGLW) compared to the others quality traits (GWT, AC, PC, and GT). Based on the GWAS analysis, a lot of QTLs have been detected for GL, GW, and RGLW (Table 1). A total of 121, 138, 81, 60, 18, 6, and 5 QTLs for GL, GW, RGLW, GWT, AC, PC, and GT; respectively have been identified by GWAS in different rice populations for almost twelve years (2010 until 2022). Many QTLs showed pleiotropic effects that control more than one quality traits on one loci. QTLs for GL more distributed on chromosome 3 than others. Meanwhile, chromosome 5 harbored more QTLs for GW. Many QTLs for RGLW displayed pleiotropic effects with QTLs for GL and GW because of their strong phenotypic correlations. QTLs for GWT mostly distributed on chromosome 7. Due to their high phenotypic correlations, QTLs for AC and GT also showed pleiotropic effects on chromosome 6. QTLs for PC distributed equally on chromosome 6, 7, 11, and 12.      

Table 1: Genome wide association studies of grain quality traits in rice.

Many genes regulating the rice grain quality traits have been cloned. About four genes controlling GL have been cloned, including PGL1 (LOC_Os03g07510) on chromosome 3, PGL2 (LOC_Os02g51320) on chromosome 2, GL3.1 (LOC_Os03g44500) on chromosome 3, and GL7/GW7 (LOC_Os07g41200) on chromosome 7 ^{66, 120, 121}. Two genes controlling GW have been cloned, including GW2 (LOC_Os02g14720) on chromosome 2 and GW8 (LOC_Os08g41940) on chromosome 8 ^{23, 122}. Genes regulating GWT that have been cloned were GW5 (LOC_Os05g09520) on chromosome 5, GW6a (LOC_Os06g44100) on chromosome 6, TGW6 (LOC_Os06g41850) on chromosome 6, and HGW (LOC_Os06g06530) on chromosome 6 ^{123, 124, 125}. The major gene regulating AC and GT is Wx on chromosome 6 ^{126, 127, 128, 129, 130, 131, 132, 133, 134, 135}. Rice which contain high AC is beneficial to be consumed by diabetic people due to their low glycemic index ^{9, 31}. These cloned genes could be effectively and efficiently used for developing high-quality rice varieties.

Environmental Stresses and Rice Grain Quality Traits

All of the rice grain quality traits, including GL, GW, RGLW, GWT, AC, PC, and GT classified as quantitative traits that controlled by multiple genes and largely affected by various environmental conditions ^{32, 36, 65}. Environmental factors that significantly affected rice grain quality traits are high-nighttime temperature (HNT), drought, and diseases ^{138, 139, 140, 141, 142}. Under HNT conditions during reproductive grain filling stages, amylose biosynthesis was down-regulated and increase percent chalkiness of the grain, and also declining grain dimensions (grain shape and size). This chalky grains decrease the grain appearance due to grains are prone to break during milling and decrease sensory characteristics ^{143, 144}. The price of broken rice grains is 50% lower than unbroken grains ^{145, 146}. Genetic improvement of rice varieties by using GWAS method are needed to develop high-quality of rice varieties in the climate change conditions and limited agricultural land, and also significantly growing population. 

Conclusions

This review article provides an insight of genetic basis of rice grain quality traits by using GWAS method to develop high-quality of rice varieties based on the rice consumers preferences. GWAS has made a great progress to provide gene resources to increase rice quality traits. Many QTLs associated with the rice grain quality traits have been identified and a lot of genes controlling grain quality traits have been cloned during twelve years (2010 until 2022). The results of this study provide important information of the genomic information associated with the rice grain quality traits to improve rice grain quality characteristics. Validation of the specific genes to improve grain quality is necessary by using transgenic strategy, gene editing techniques, gene expression analyses, and fine-mapped based cloning.

Conflicts of interest

I have no conflict of interest.

Funding Sources

There is no funding sources

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